library(multiMiR)
## Welcome to multiMiR.
## 
## multiMiR database URL has been set to the 
## default value: http://multimir.org/
## 
## Database Version: 2.3.0  Updated: 2020-04-15
library(clusterProfiler)
## 
## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
## 
## Please cite:
## 
## S Xu, E Hu, Y Cai, Z Xie, X Luo, L Zhan, W Tang, Q Wang, B Liu, R Wang,
## W Xie, T Wu, L Xie, G Yu. Using clusterProfiler to characterize
## multiomics data. Nature Protocols. 2024, doi:10.1038/s41596-024-01020-z
## 
## Attaching package: 'clusterProfiler'
## The following object is masked from 'package:multiMiR':
## 
##     select
## The following object is masked from 'package:stats':
## 
##     filter
library(org.Hs.eg.db)
## Loading required package: AnnotationDbi
## Loading required package: stats4
## Loading required package: BiocGenerics
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs
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##     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
##     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
##     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
##     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
##     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
##     tapply, union, unique, unsplit, which.max, which.min
## Loading required package: Biobase
## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
## Loading required package: IRanges
## Loading required package: S4Vectors
## 
## Attaching package: 'S4Vectors'
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##     rename
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##     expand.grid, I, unname
## 
## Attaching package: 'IRanges'
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##     slice
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##     windows
## 
## Attaching package: 'AnnotationDbi'
## The following object is masked from 'package:clusterProfiler':
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##     select
## 
library(stringr)
library(ggplot2)

0. Loading of Results

A. List of all Gene names in the dataset

gene.names = readRDS("data/derived/unique_gene_names.rds")

B. Selected Features

results.superbiclust.fabia20 = readRDS("data/sel_features/results_superbiclust.fabia.rds")
sel.features = results.superbiclust.fabia20$resNames
sel.features
## [[1]]
##  [1] "hsa-mir-1185-1" "hsa-mir-1185-2" "hsa-mir-1197"   "hsa-mir-323"   
##  [5] "hsa-mir-329-1"  "hsa-mir-329-2"  "hsa-mir-370"    "hsa-mir-376a-1"
##  [9] "hsa-mir-377"    "hsa-mir-380"    "hsa-mir-433"    "hsa-mir-487a"  
## [13] "hsa-mir-496"    "hsa-mir-541"    "hsa-mir-654"    "hsa-mir-655"   
## [17] "hsa-mir-656"    "hsa-mir-668"    "hsa-mir-770"   
## 
## [[2]]
##  [1] "hsa-mir-1185-1" "hsa-mir-1185-2" "hsa-mir-1197"   "hsa-mir-127"   
##  [5] "hsa-mir-134"    "hsa-mir-136"    "hsa-mir-154"    "hsa-mir-323"   
##  [9] "hsa-mir-323b"   "hsa-mir-329-1"  "hsa-mir-329-2"  "hsa-mir-370"   
## [13] "hsa-mir-376a-1" "hsa-mir-376a-2" "hsa-mir-376c"   "hsa-mir-377"   
## [17] "hsa-mir-380"    "hsa-mir-382"    "hsa-mir-409"    "hsa-mir-433"   
## [21] "hsa-mir-487a"   "hsa-mir-487b"   "hsa-mir-494"    "hsa-mir-496"   
## [25] "hsa-mir-539"    "hsa-mir-541"    "hsa-mir-654"    "hsa-mir-655"   
## [29] "hsa-mir-656"    "hsa-mir-665"    "hsa-mir-668"    "hsa-mir-770"   
## [33] "hsa-mir-889"   
## 
## [[3]]
##  [1] "hsa-mir-506"    "hsa-mir-507"    "hsa-mir-508"    "hsa-mir-509-1" 
##  [5] "hsa-mir-509-2"  "hsa-mir-509-3"  "hsa-mir-510"    "hsa-mir-513a-1"
##  [9] "hsa-mir-513a-2" "hsa-mir-513b"   "hsa-mir-513c"   "hsa-mir-514-1" 
## [13] "hsa-mir-514-2"  "hsa-mir-514-3" 
## 
## [[4]]
##  [1] "hsa-mir-1185-1" "hsa-mir-1185-2" "hsa-mir-1197"   "hsa-mir-127"   
##  [5] "hsa-mir-134"    "hsa-mir-154"    "hsa-mir-299"    "hsa-mir-323"   
##  [9] "hsa-mir-323b"   "hsa-mir-329-1"  "hsa-mir-329-2"  "hsa-mir-370"   
## [13] "hsa-mir-376a-1" "hsa-mir-376c"   "hsa-mir-377"    "hsa-mir-380"   
## [17] "hsa-mir-382"    "hsa-mir-409"    "hsa-mir-411"    "hsa-mir-485"   
## [21] "hsa-mir-487a"   "hsa-mir-494"    "hsa-mir-496"    "hsa-mir-541"   
## [25] "hsa-mir-543"    "hsa-mir-654"    "hsa-mir-655"    "hsa-mir-656"   
## [29] "hsa-mir-668"    "hsa-mir-770"    "hsa-mir-889"   
## 
## [[5]]
##  [1] "hsa-mir-1185-1" "hsa-mir-1185-2" "hsa-mir-329-1"  "hsa-mir-329-2" 
##  [5] "hsa-mir-380"    "hsa-mir-487a"   "hsa-mir-655"    "hsa-mir-656"   
##  [9] "hsa-mir-665"    "hsa-mir-770"   
## 
## [[6]]
## [1] "hsa-mir-517a" "hsa-mir-518b"
## 
## [[7]]
## [1] "hsa-mir-876"
## 
## [[8]]
## [1] "hsa-mir-507"    "hsa-mir-509-1"  "hsa-mir-509-2"  "hsa-mir-510"   
## [5] "hsa-mir-513a-2"
## 
## [[9]]
## [1] "hsa-mir-1185-1" "hsa-mir-380"    "hsa-mir-487a"   "hsa-mir-655"   
## [5] "hsa-mir-656"   
## 
## [[10]]
## [1] "hsa-mir-507" "hsa-mir-510"
## 
## [[11]]
## character(0)
## 
## [[12]]
## [1] "FN1.R2Gn"
## 
## [[13]]
## [1] "hsa-mir-510"
## 
## [[14]]
## [1] "hsa-mir-656"
## 
## [[15]]
## character(0)
## 
## [[16]]
##  [1] "hsa-mir-1185-1" "hsa-mir-1185-2" "hsa-mir-329-1"  "hsa-mir-329-2" 
##  [5] "hsa-mir-370"    "hsa-mir-376a-1" "hsa-mir-377"    "hsa-mir-380"   
##  [9] "hsa-mir-411"    "hsa-mir-433"    "hsa-mir-487a"   "hsa-mir-494"   
## [13] "hsa-mir-541"    "hsa-mir-655"    "hsa-mir-656"    "hsa-mir-665"   
## [17] "hsa-mir-668"    "hsa-mir-770"   
## 
## [[17]]
## character(0)
## 
## [[18]]
## [1] "G6PD.RPPA"
## 
## [[19]]
## character(0)
## 
## [[20]]
## character(0)
## 
## [[21]]
## character(0)
## 
## [[22]]
## [1] "GAPDH.R2Gn"
## 
## [[23]]
## character(0)
## 
## [[24]]
## character(0)
## 
## [[25]]
## character(0)
## 
## [[26]]
## [1] "CTNNB1.R2Gn"
## 
## [[27]]
## character(0)
## 
## [[28]]
## [1] "TGM2.R2Gn"
## 
## [[29]]
## character(0)
## 
## [[30]]
## character(0)
## 
## [[31]]
## character(0)

1. Convert microRNA to genes

Also remove the ending “.R2Gn” and “.RPPA” from gene names.

split.by.omic = function(variable.list) {
  out.mRSG = variable.list[startsWith(variable.list, "hsa")]
  out.R2Gn = variable.list[endsWith(variable.list, "R2Gn")]
  out.RPPA = variable.list[endsWith(variable.list, "RPPA")]
  out = list("miRNASeqGene" = out.mRSG,
             "RNASeq2GeneNorm" = out.R2Gn,
             "RPPAArray" = out.RPPA)
  out
}
multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
  multiomics.list = split.by.omic(sel.features)
  # Convert miRNASeqGene to target GENE names
  # Skipped and returns an empty list instead of the list of select features,
  # or if microRNA features are explicitly dropped (drop.miRNA = T).
  # (Usually done when the features has only a few miRNA and unable to target any genes)
  if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
    if (!full.search) { # Search only among the 198 genes in ACC, recommended
    targets= get_multimir(mirna = multiomics.list[[1]], 
                          target = gene.names,
                          table = table,
                          summary = T)
    mRSG.target.genes = unique(targets@data$target_symbol)
    } else { # Search the full dataset, not recommended. 
             # Use only if ACC gene search returns nothing or fails.
             # Genes not in the ACC genes need to be manually removed.
    targets= get_multimir(mirna = multiomics.list[[1]], 
                          table = table,
                          summary = T)  
    mRSG.target.genes = unique(targets@data$target_symbol)
    }
    
  } else {
    mRSG.target.genes = list()
  }
  #Remove suffix for Pathway Analysis Compatibility
  R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
  
  RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
  
  #Join all cleaned-up genes are remove duplicates.
  out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes)
  out = as.character(unique(out1))
  out
}
geneNames <- list("biclust1"=multiomics.to.GENES(sel.features[[1]]),
                  "biclust2"=multiomics.to.GENES(sel.features[[2]]),
                  "biclust3"=multiomics.to.GENES(sel.features[[3]]),
                  "biclust4"=multiomics.to.GENES(sel.features[[4]]),
                  "biclust5"=multiomics.to.GENES(sel.features[[5]]),
                  #"biclust6"=multiomics.to.GENES(sel.features[[6]], table = "all"), # Only works with table = "all", removed
                  #"biclust7"=multiomics.to.GENES(sel.features[[7]], full.search = T), #No results found, error
                  "biclust8"=multiomics.to.GENES(sel.features[[8]]),
                  #"biclust9"=multiomics.to.GENES(sel.features[[9]], full.search = T), #No results found, error
                  "biclust10"=multiomics.to.GENES(sel.features[[10]]),
                  "biclust12"=multiomics.to.GENES(sel.features[[12]]),
                  #"biclust13"=multiomics.to.GENES(sel.features[[13]], full.search = T), #No results found, error
                  #"biclust14"=multiomics.to.GENES(sel.features[[14]], full.search = T), #No results found, error
                  "biclust16"=multiomics.to.GENES(sel.features[[16]]),
                  "biclust18"=multiomics.to.GENES(sel.features[[18]]),
                  "biclust22"=multiomics.to.GENES(sel.features[[22]]),
                  "biclust26"=multiomics.to.GENES(sel.features[[26]]),
                  "biclust28"=multiomics.to.GENES(sel.features[[28]]))
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
## Searching mirecords ...
## Searching mirtarbase ...
## Searching tarbase ...
geneNames
## $biclust1
## [1] "HSPA1A" "AKT1"   "VHL"    "MTOR"   "MAPK8"  "CDKN1A" "STAT5A"
## 
## $biclust2
##  [1] "HSPA1A" "AKT1"   "VHL"    "MTOR"   "MAPK8"  "MYH9"   "CDKN1A" "FOXO3" 
##  [9] "ATM"    "CASP8"  "MACC1"  "STAT5A" "CCND1"  "YAP1"   "MAPK1"  "ANLN"  
## 
## $biclust3
## [1] "ETS1"   "XIAP"   "MAPK8"  "ARID1A" "BID"    "NCOA3"  "GAB2"  
## 
## $biclust4
##  [1] "HSPA1A" "AKT1"   "VHL"    "MTOR"   "MAPK8"  "PTEN"   "KRAS"   "NRAS"  
##  [9] "PTK2"   "ETS1"   "ATM"    "CDKN1A" "STAT5A" "ITGA2" 
## 
## $biclust5
##  [1] "MYH9"   "CDKN1A" "FOXO3"  "ATM"    "CASP8"  "MACC1"  "CCND1"  "YAP1"  
##  [9] "MAPK1"  "ANLN"  
## 
## $biclust8
## [1] "ETS1"   "XIAP"   "MAPK8"  "ARID1A" "BID"    "NCOA3"  "GAB2"  
## 
## $biclust10
## [1] "ETS1"   "XIAP"   "MAPK8"  "ARID1A" "BID"    "NCOA3"  "GAB2"  
## 
## $biclust12
## [1] "FN1"
## 
## $biclust16
##  [1] "MYH9"   "CDKN1A" "FOXO3"  "ATM"    "CASP8"  "MACC1"  "CCND1"  "YAP1"  
##  [9] "MAPK1"  "ANLN"  
## 
## $biclust18
## [1] "G6PD"
## 
## $biclust22
## [1] "GAPDH"
## 
## $biclust26
## [1] "CTNNB1"
## 
## $biclust28
## [1] "TGM2"
saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_superbiclust.fabia.rds")

2. Pathway Analysis

A. GO Classification

ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component


for(z in 1:length(geneNames)){
  print(z)
  input <- geneNames[[z]]

  ggo_MF[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="MF",
    keyType="SYMBOL",
    readable=TRUE)
  
  ggo_BP[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="BP",
    keyType="SYMBOL",
    readable=TRUE)

  ggo_CC[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="CC",
    keyType="SYMBOL",
    readable=TRUE)    
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
## [1] 13
for(z in 1:length(geneNames)) {
  print(head(ggo_MF[[z]]))
  print(head(ggo_BP[[z]]))
  print(head(ggo_CC[[z]]))
}
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/7
## GO:0003824 GO:0003824           catalytic activity     6       6/7
## GO:0005198 GO:0005198 structural molecule activity     0       0/7
## GO:0005215 GO:0005215         transporter activity     0       0/7
## GO:0005488 GO:0005488                      binding     7       7/7
## GO:0009055 GO:0009055   electron transfer activity     0       0/7
##                                              geneID
## GO:0003774                                         
## GO:0003824        HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A
## GO:0005198                                         
## GO:0005215                                         
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/STAT5A
## GO:0009055                                         
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     2       2/7
## GO:0002376 GO:0002376 immune system process     5       5/7
## GO:0008152 GO:0008152     metabolic process     7       7/7
## GO:0009987 GO:0009987      cellular process     7       7/7
## GO:0016032 GO:0016032         viral process     2       2/7
## GO:0022414 GO:0022414  reproductive process     2       2/7
##                                              geneID
## GO:0000003                                AKT1/MTOR
## GO:0002376            HSPA1A/AKT1/MTOR/MAPK8/CDKN1A
## GO:0008152 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/STAT5A
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/STAT5A
## GO:0016032                              HSPA1A/AKT1
## GO:0022414                                AKT1/MTOR
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     5       5/7
## GO:0044423 GO:0044423           virion component     0       0/7
## GO:0110165 GO:0110165 cellular anatomical entity     7       7/7
##                                              geneID
## GO:0032991           HSPA1A/AKT1/MTOR/CDKN1A/STAT5A
## GO:0044423                                         
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/STAT5A
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/16
## GO:0003824 GO:0003824           catalytic activity    10     10/16
## GO:0005198 GO:0005198 structural molecule activity     0      0/16
## GO:0005215 GO:0005215         transporter activity     0      0/16
## GO:0005488 GO:0005488                      binding    16     16/16
## GO:0009055 GO:0009055   electron transfer activity     0      0/16
##                                                                                               geneID
## GO:0003774                                                                                      MYH9
## GO:0003824                                   HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/CCND1/MAPK1
## GO:0005198                                                                                          
## GO:0005215                                                                                          
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/STAT5A/CCND1/YAP1/MAPK1/ANLN
## GO:0009055                                                                                          
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     6      6/16
## GO:0002376 GO:0002376 immune system process    10     10/16
## GO:0008152 GO:0008152     metabolic process    15     15/16
## GO:0009987 GO:0009987      cellular process    16     16/16
## GO:0016032 GO:0016032         viral process     2      2/16
## GO:0022414 GO:0022414  reproductive process     6      6/16
##                                                                                               geneID
## GO:0000003                                                            AKT1/MTOR/MYH9/FOXO3/ATM/CASP8
## GO:0002376                                  HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MAPK1
## GO:0008152      HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/STAT5A/CCND1/YAP1/MAPK1
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/STAT5A/CCND1/YAP1/MAPK1/ANLN
## GO:0016032                                                                               HSPA1A/AKT1
## GO:0022414                                                            AKT1/MTOR/MYH9/FOXO3/ATM/CASP8
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    11     11/16
## GO:0044423 GO:0044423           virion component     0      0/16
## GO:0110165 GO:0110165 cellular anatomical entity    16     16/16
##                                                                                               geneID
## GO:0032991                            HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/STAT5A/CCND1/YAP1
## GO:0044423                                                                                          
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/STAT5A/CCND1/YAP1/MAPK1/ANLN
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/7
## GO:0003824 GO:0003824           catalytic activity     3       3/7
## GO:0005198 GO:0005198 structural molecule activity     0       0/7
## GO:0005215 GO:0005215         transporter activity     0       0/7
## GO:0005488 GO:0005488                      binding     7       7/7
## GO:0009055 GO:0009055   electron transfer activity     0       0/7
##                                           geneID
## GO:0003774                                      
## GO:0003824                      XIAP/MAPK8/NCOA3
## GO:0005198                                      
## GO:0005215                                      
## GO:0005488 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
## GO:0009055                                      
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     0       0/7
## GO:0002376 GO:0002376 immune system process     6       6/7
## GO:0008152 GO:0008152     metabolic process     6       6/7
## GO:0009987 GO:0009987      cellular process     7       7/7
## GO:0016032 GO:0016032         viral process     0       0/7
## GO:0022414 GO:0022414  reproductive process     0       0/7
##                                           geneID
## GO:0000003                                      
## GO:0002376       ETS1/XIAP/MAPK8/ARID1A/BID/GAB2
## GO:0008152      ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3
## GO:0009987 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
## GO:0016032                                      
## GO:0022414                                      
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     3       3/7
## GO:0044423 GO:0044423           virion component     0       0/7
## GO:0110165 GO:0110165 cellular anatomical entity     7       7/7
##                                           geneID
## GO:0032991                     ETS1/ARID1A/NCOA3
## GO:0044423                                      
## GO:0110165 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/14
## GO:0003824 GO:0003824           catalytic activity    11     11/14
## GO:0005198 GO:0005198 structural molecule activity     0      0/14
## GO:0005215 GO:0005215         transporter activity     0      0/14
## GO:0005488 GO:0005488                      binding    14     14/14
## GO:0009055 GO:0009055   electron transfer activity     0      0/14
##                                                                                 geneID
## GO:0003774                                                                            
## GO:0003824                   HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/NRAS/PTK2/ATM/CDKN1A
## GO:0005198                                                                            
## GO:0005215                                                                            
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/NRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/ITGA2
## GO:0009055                                                                            
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     5      5/14
## GO:0002376 GO:0002376 immune system process     9      9/14
## GO:0008152 GO:0008152     metabolic process    13     13/14
## GO:0009987 GO:0009987      cellular process    14     14/14
## GO:0016032 GO:0016032         viral process     3      3/14
## GO:0022414 GO:0022414  reproductive process     5      5/14
##                                                                                 geneID
## GO:0000003                                                    AKT1/MTOR/PTEN/ATM/ITGA2
## GO:0002376                           HSPA1A/AKT1/MTOR/MAPK8/PTK2/ETS1/ATM/CDKN1A/ITGA2
## GO:0008152      HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/ITGA2
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/NRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/ITGA2
## GO:0016032                                                           HSPA1A/AKT1/ITGA2
## GO:0022414                                                    AKT1/MTOR/PTEN/ATM/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     8      8/14
## GO:0044423 GO:0044423           virion component     0      0/14
## GO:0110165 GO:0110165 cellular anatomical entity    14     14/14
##                                                                                 geneID
## GO:0032991                               HSPA1A/AKT1/MTOR/ETS1/ATM/CDKN1A/STAT5A/ITGA2
## GO:0044423                                                                            
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/NRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/ITGA2
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/10
## GO:0003824 GO:0003824           catalytic activity     5      5/10
## GO:0005198 GO:0005198 structural molecule activity     0      0/10
## GO:0005215 GO:0005215         transporter activity     0      0/10
## GO:0005488 GO:0005488                      binding    10     10/10
## GO:0009055 GO:0009055   electron transfer activity     0      0/10
##                                                             geneID
## GO:0003774                                                    MYH9
## GO:0003824                            CDKN1A/ATM/CASP8/CCND1/MAPK1
## GO:0005198                                                        
## GO:0005215                                                        
## GO:0005488 MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/YAP1/MAPK1/ANLN
## GO:0009055                                                        
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     4      4/10
## GO:0002376 GO:0002376 immune system process     6      6/10
## GO:0008152 GO:0008152     metabolic process     9      9/10
## GO:0009987 GO:0009987      cellular process    10     10/10
## GO:0016032 GO:0016032         viral process     0      0/10
## GO:0022414 GO:0022414  reproductive process     4      4/10
##                                                             geneID
## GO:0000003                                    MYH9/FOXO3/ATM/CASP8
## GO:0002376                       MYH9/CDKN1A/FOXO3/ATM/CASP8/MAPK1
## GO:0008152      MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/YAP1/MAPK1
## GO:0009987 MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/YAP1/MAPK1/ANLN
## GO:0016032                                                        
## GO:0022414                                    MYH9/FOXO3/ATM/CASP8
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     7      7/10
## GO:0044423 GO:0044423           virion component     0      0/10
## GO:0110165 GO:0110165 cellular anatomical entity    10     10/10
##                                                             geneID
## GO:0032991                  MYH9/CDKN1A/FOXO3/ATM/CASP8/CCND1/YAP1
## GO:0044423                                                        
## GO:0110165 MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/YAP1/MAPK1/ANLN
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/7
## GO:0003824 GO:0003824           catalytic activity     3       3/7
## GO:0005198 GO:0005198 structural molecule activity     0       0/7
## GO:0005215 GO:0005215         transporter activity     0       0/7
## GO:0005488 GO:0005488                      binding     7       7/7
## GO:0009055 GO:0009055   electron transfer activity     0       0/7
##                                           geneID
## GO:0003774                                      
## GO:0003824                      XIAP/MAPK8/NCOA3
## GO:0005198                                      
## GO:0005215                                      
## GO:0005488 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
## GO:0009055                                      
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     0       0/7
## GO:0002376 GO:0002376 immune system process     6       6/7
## GO:0008152 GO:0008152     metabolic process     6       6/7
## GO:0009987 GO:0009987      cellular process     7       7/7
## GO:0016032 GO:0016032         viral process     0       0/7
## GO:0022414 GO:0022414  reproductive process     0       0/7
##                                           geneID
## GO:0000003                                      
## GO:0002376       ETS1/XIAP/MAPK8/ARID1A/BID/GAB2
## GO:0008152      ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3
## GO:0009987 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
## GO:0016032                                      
## GO:0022414                                      
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     3       3/7
## GO:0044423 GO:0044423           virion component     0       0/7
## GO:0110165 GO:0110165 cellular anatomical entity     7       7/7
##                                           geneID
## GO:0032991                     ETS1/ARID1A/NCOA3
## GO:0044423                                      
## GO:0110165 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/7
## GO:0003824 GO:0003824           catalytic activity     3       3/7
## GO:0005198 GO:0005198 structural molecule activity     0       0/7
## GO:0005215 GO:0005215         transporter activity     0       0/7
## GO:0005488 GO:0005488                      binding     7       7/7
## GO:0009055 GO:0009055   electron transfer activity     0       0/7
##                                           geneID
## GO:0003774                                      
## GO:0003824                      XIAP/MAPK8/NCOA3
## GO:0005198                                      
## GO:0005215                                      
## GO:0005488 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
## GO:0009055                                      
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     0       0/7
## GO:0002376 GO:0002376 immune system process     6       6/7
## GO:0008152 GO:0008152     metabolic process     6       6/7
## GO:0009987 GO:0009987      cellular process     7       7/7
## GO:0016032 GO:0016032         viral process     0       0/7
## GO:0022414 GO:0022414  reproductive process     0       0/7
##                                           geneID
## GO:0000003                                      
## GO:0002376       ETS1/XIAP/MAPK8/ARID1A/BID/GAB2
## GO:0008152      ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3
## GO:0009987 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
## GO:0016032                                      
## GO:0022414                                      
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     3       3/7
## GO:0044423 GO:0044423           virion component     0       0/7
## GO:0110165 GO:0110165 cellular anatomical entity     7       7/7
##                                           geneID
## GO:0032991                     ETS1/ARID1A/NCOA3
## GO:0044423                                      
## GO:0110165 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
##                    ID                  Description Count GeneRatio geneID
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/1       
## GO:0003824 GO:0003824           catalytic activity     0       0/1       
## GO:0005198 GO:0005198 structural molecule activity     1       1/1    FN1
## GO:0005215 GO:0005215         transporter activity     0       0/1       
## GO:0005488 GO:0005488                      binding     1       1/1    FN1
## GO:0009055 GO:0009055   electron transfer activity     0       0/1       
##                    ID           Description Count GeneRatio geneID
## GO:0000003 GO:0000003          reproduction     0       0/1       
## GO:0002376 GO:0002376 immune system process     1       1/1    FN1
## GO:0008152 GO:0008152     metabolic process     1       1/1    FN1
## GO:0009987 GO:0009987      cellular process     1       1/1    FN1
## GO:0016032 GO:0016032         viral process     0       0/1       
## GO:0022414 GO:0022414  reproductive process     0       0/1       
##                    ID                Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex     1       1/1    FN1
## GO:0044423 GO:0044423           virion component     0       0/1       
## GO:0110165 GO:0110165 cellular anatomical entity     1       1/1    FN1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/10
## GO:0003824 GO:0003824           catalytic activity     5      5/10
## GO:0005198 GO:0005198 structural molecule activity     0      0/10
## GO:0005215 GO:0005215         transporter activity     0      0/10
## GO:0005488 GO:0005488                      binding    10     10/10
## GO:0009055 GO:0009055   electron transfer activity     0      0/10
##                                                             geneID
## GO:0003774                                                    MYH9
## GO:0003824                            CDKN1A/ATM/CASP8/CCND1/MAPK1
## GO:0005198                                                        
## GO:0005215                                                        
## GO:0005488 MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/YAP1/MAPK1/ANLN
## GO:0009055                                                        
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     4      4/10
## GO:0002376 GO:0002376 immune system process     6      6/10
## GO:0008152 GO:0008152     metabolic process     9      9/10
## GO:0009987 GO:0009987      cellular process    10     10/10
## GO:0016032 GO:0016032         viral process     0      0/10
## GO:0022414 GO:0022414  reproductive process     4      4/10
##                                                             geneID
## GO:0000003                                    MYH9/FOXO3/ATM/CASP8
## GO:0002376                       MYH9/CDKN1A/FOXO3/ATM/CASP8/MAPK1
## GO:0008152      MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/YAP1/MAPK1
## GO:0009987 MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/YAP1/MAPK1/ANLN
## GO:0016032                                                        
## GO:0022414                                    MYH9/FOXO3/ATM/CASP8
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     7      7/10
## GO:0044423 GO:0044423           virion component     0      0/10
## GO:0110165 GO:0110165 cellular anatomical entity    10     10/10
##                                                             geneID
## GO:0032991                  MYH9/CDKN1A/FOXO3/ATM/CASP8/CCND1/YAP1
## GO:0044423                                                        
## GO:0110165 MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/YAP1/MAPK1/ANLN
##                    ID                  Description Count GeneRatio geneID
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/1       
## GO:0003824 GO:0003824           catalytic activity     1       1/1   G6PD
## GO:0005198 GO:0005198 structural molecule activity     0       0/1       
## GO:0005215 GO:0005215         transporter activity     0       0/1       
## GO:0005488 GO:0005488                      binding     1       1/1   G6PD
## GO:0009055 GO:0009055   electron transfer activity     0       0/1       
##                    ID           Description Count GeneRatio geneID
## GO:0000003 GO:0000003          reproduction     0       0/1       
## GO:0002376 GO:0002376 immune system process     1       1/1   G6PD
## GO:0008152 GO:0008152     metabolic process     1       1/1   G6PD
## GO:0009987 GO:0009987      cellular process     1       1/1   G6PD
## GO:0016032 GO:0016032         viral process     0       0/1       
## GO:0022414 GO:0022414  reproductive process     0       0/1       
##                    ID                Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex     0       0/1       
## GO:0044423 GO:0044423           virion component     0       0/1       
## GO:0110165 GO:0110165 cellular anatomical entity     1       1/1   G6PD
##                    ID                  Description Count GeneRatio geneID
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/1       
## GO:0003824 GO:0003824           catalytic activity     1       1/1  GAPDH
## GO:0005198 GO:0005198 structural molecule activity     0       0/1       
## GO:0005215 GO:0005215         transporter activity     0       0/1       
## GO:0005488 GO:0005488                      binding     1       1/1  GAPDH
## GO:0009055 GO:0009055   electron transfer activity     0       0/1       
##                    ID           Description Count GeneRatio geneID
## GO:0000003 GO:0000003          reproduction     0       0/1       
## GO:0002376 GO:0002376 immune system process     1       1/1  GAPDH
## GO:0008152 GO:0008152     metabolic process     1       1/1  GAPDH
## GO:0009987 GO:0009987      cellular process     1       1/1  GAPDH
## GO:0016032 GO:0016032         viral process     0       0/1       
## GO:0022414 GO:0022414  reproductive process     0       0/1       
##                    ID                Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex     1       1/1  GAPDH
## GO:0044423 GO:0044423           virion component     0       0/1       
## GO:0110165 GO:0110165 cellular anatomical entity     1       1/1  GAPDH
##                    ID                  Description Count GeneRatio geneID
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/1       
## GO:0003824 GO:0003824           catalytic activity     0       0/1       
## GO:0005198 GO:0005198 structural molecule activity     0       0/1       
## GO:0005215 GO:0005215         transporter activity     0       0/1       
## GO:0005488 GO:0005488                      binding     1       1/1 CTNNB1
## GO:0009055 GO:0009055   electron transfer activity     0       0/1       
##                    ID           Description Count GeneRatio geneID
## GO:0000003 GO:0000003          reproduction     1       1/1 CTNNB1
## GO:0002376 GO:0002376 immune system process     1       1/1 CTNNB1
## GO:0008152 GO:0008152     metabolic process     1       1/1 CTNNB1
## GO:0009987 GO:0009987      cellular process     1       1/1 CTNNB1
## GO:0016032 GO:0016032         viral process     0       0/1       
## GO:0022414 GO:0022414  reproductive process     1       1/1 CTNNB1
##                    ID                Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex     1       1/1 CTNNB1
## GO:0044423 GO:0044423           virion component     0       0/1       
## GO:0110165 GO:0110165 cellular anatomical entity     1       1/1 CTNNB1
##                    ID                  Description Count GeneRatio geneID
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/1       
## GO:0003824 GO:0003824           catalytic activity     1       1/1   TGM2
## GO:0005198 GO:0005198 structural molecule activity     0       0/1       
## GO:0005215 GO:0005215         transporter activity     0       0/1       
## GO:0005488 GO:0005488                      binding     1       1/1   TGM2
## GO:0009055 GO:0009055   electron transfer activity     0       0/1       
##                    ID           Description Count GeneRatio geneID
## GO:0000003 GO:0000003          reproduction     0       0/1       
## GO:0002376 GO:0002376 immune system process     0       0/1       
## GO:0008152 GO:0008152     metabolic process     1       1/1   TGM2
## GO:0009987 GO:0009987      cellular process     1       1/1   TGM2
## GO:0016032 GO:0016032         viral process     0       0/1       
## GO:0022414 GO:0022414  reproductive process     0       0/1       
##                    ID                Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex     1       1/1   TGM2
## GO:0044423 GO:0044423           virion component     0       0/1       
## GO:0110165 GO:0110165 cellular anatomical entity     1       1/1   TGM2
barplot(ggo_MF[[1]], title = "graphGO, Molecular Function, bicluster 1")

barplot(ggo_MF[[2]], title = "graphGO, Molecular Function, bicluster 2")

barplot(ggo_MF[[3]], title = "graphGO, Molecular Function, bicluster 3")

barplot(ggo_MF[[4]], title = "graphGO, Molecular Function, bicluster 4")

barplot(ggo_MF[[5]], title = "graphGO, Molecular Function, bicluster 5")

barplot(ggo_MF[[6]], title = "graphGO, Molecular Function, bicluster 8")

barplot(ggo_MF[[7]], title = "graphGO, Molecular Function, bicluster 10")

barplot(ggo_MF[[8]], title = "graphGO, Molecular Function, bicluster 12")

barplot(ggo_MF[[9]], title = "graphGO, Molecular Function, bicluster 16")

barplot(ggo_MF[[10]], title = "graphGO, Molecular Function, bicluster 18")

barplot(ggo_MF[[11]], title = "graphGO, Molecular Function, bicluster 22")

barplot(ggo_MF[[12]], title = "graphGO, Molecular Function, bicluster 26")

barplot(ggo_MF[[13]], title = "graphGO, Molecular Function, bicluster 28")

barplot(ggo_BP[[1]], title = "graphGO, Biological Process, bicluster 1")

barplot(ggo_BP[[2]], title = "graphGO, Biological Process, bicluster 2")

barplot(ggo_BP[[3]], title = "graphGO, Biological Process, bicluster 3")

barplot(ggo_BP[[4]], title = "graphGO, Biological Process, bicluster 4")

barplot(ggo_BP[[5]], title = "graphGO, Biological Process, bicluster 5")

barplot(ggo_BP[[6]], title = "graphGO, Biological Process, bicluster 8")

barplot(ggo_BP[[7]], title = "graphGO, Biological Process, bicluster 10")

barplot(ggo_BP[[8]], title = "graphGO, Biological Process, bicluster 12")

barplot(ggo_BP[[9]], title = "graphGO, Biological Process, bicluster 16")

barplot(ggo_BP[[10]], title = "graphGO, Biological Process, bicluster 18")

barplot(ggo_BP[[11]], title = "graphGO, Biological Process, bicluster 22")

barplot(ggo_BP[[12]], title = "graphGO, Biological Process, bicluster 26")

barplot(ggo_BP[[13]], title = "graphGO, Biological Process, bicluster 28")

barplot(ggo_CC[[1]], title = "graphGO, Cellular Component, bicluster 1")

barplot(ggo_CC[[2]], title = "graphGO, Cellular Component, bicluster 2")

barplot(ggo_CC[[3]], title = "graphGO, Cellular Component, bicluster 3")

barplot(ggo_CC[[4]], title = "graphGO, Cellular Component, bicluster 4")

barplot(ggo_CC[[5]], title = "graphGO, Cellular Component, bicluster 5")

barplot(ggo_CC[[6]], title = "graphGO, Cellular Component, bicluster 8")

barplot(ggo_CC[[7]], title = "graphGO, Cellular Component, bicluster 10")

barplot(ggo_CC[[8]], title = "graphGO, Cellular Component, bicluster 12")

barplot(ggo_CC[[9]], title = "graphGO, Cellular Component, bicluster 16")

barplot(ggo_CC[[10]], title = "graphGO, Cellular Component, bicluster 18")

barplot(ggo_CC[[11]], title = "graphGO, Cellular Component, bicluster 22")

barplot(ggo_CC[[12]], title = "graphGO, Cellular Component, bicluster 26")

barplot(ggo_CC[[13]], title = "graphGO, Cellular Component, bicluster 28")

B. GO Over-Representation

ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Molecular Function
ego_CC <- list()#GO enrichment of a geneset for Molecular Function


for(z in 1:length(geneNames)){
  print(z)
  input <- geneNames[[z]]
  ego_MF[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "MF",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
  
  ego_BP[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "BP",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
  
  ego_CC[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "CC",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
## [1] 13
for(z in 1:length(geneNames)){
  print(head(ego_MF[[z]]))
  print(head(ego_BP[[z]]))
  print(head(ego_CC[[z]]))
}
##                    ID                                        Description
## GO:0030291 GO:0030291 protein serine/threonine kinase inhibitor activity
## GO:0106310 GO:0106310                     protein serine kinase activity
## GO:0004860 GO:0004860                  protein kinase inhibitor activity
## GO:0019210 GO:0019210                          kinase inhibitor activity
## GO:0004674 GO:0004674           protein serine/threonine kinase activity
## GO:0001156 GO:0001156  TFIIIC-class transcription factor complex binding
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0030291       2/7  37/18522 8.102785e-05 0.006199945 0.001506060
## GO:0106310       3/7 363/18522 2.464449e-04 0.006199945 0.001506060
## GO:0004860       2/7  73/18522 3.176644e-04 0.006199945 0.001506060
## GO:0019210       2/7  78/18522 3.626662e-04 0.006199945 0.001506060
## GO:0004674       3/7 427/18522 3.974324e-04 0.006199945 0.001506060
## GO:0001156       1/7   2/18522 7.557355e-04 0.006314766 0.001533951
##                     geneID Count
## GO:0030291     AKT1/CDKN1A     2
## GO:0106310 AKT1/MTOR/MAPK8     3
## GO:0004860     AKT1/CDKN1A     2
## GO:0019210     AKT1/CDKN1A     2
## GO:0004674 AKT1/MTOR/MAPK8     3
## GO:0001156            MTOR     1
##                    ID                                Description GeneRatio
## GO:0009408 GO:0009408                           response to heat       4/7
## GO:0009266 GO:0009266           response to temperature stimulus       4/7
## GO:0034198 GO:0034198 cellular response to amino acid starvation       3/7
## GO:1990928 GO:1990928          response to amino acid starvation       3/7
## GO:0034605 GO:0034605                  cellular response to heat       3/7
## GO:0032091 GO:0032091     negative regulation of protein binding       3/7
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0009408 104/18888 2.997255e-08 3.380904e-05 7.982164e-06
## GO:0009266 172/18888 2.275196e-07 1.283210e-04 3.029602e-05
## GO:0034198  51/18888 6.441709e-07 2.162617e-04 5.105843e-05
## GO:1990928  54/18888 7.668854e-07 2.162617e-04 5.105843e-05
## GO:0034605  67/18888 1.478057e-06 3.313185e-04 7.822283e-05
## GO:0032091  71/18888 1.762333e-06 3.313185e-04 7.822283e-05
##                             geneID Count
## GO:0009408 HSPA1A/AKT1/MTOR/CDKN1A     4
## GO:0009266 HSPA1A/AKT1/MTOR/CDKN1A     4
## GO:0034198       MTOR/MAPK8/CDKN1A     3
## GO:1990928       MTOR/MAPK8/CDKN1A     3
## GO:0034605      HSPA1A/MTOR/CDKN1A     3
## GO:0032091       AKT1/MAPK8/CDKN1A     3
##                    ID      Description GeneRatio  BgRatio       pvalue
## GO:0070557 GO:0070557 PCNA-p21 complex       1/7  2/19894 0.0007036236
## GO:0031931 GO:0031931    TORC1 complex       1/7  6/19894 0.0021095979
## GO:0097441 GO:0097441   basal dendrite       1/7  6/19894 0.0021095979
## GO:0031932 GO:0031932    TORC2 complex       1/7  9/19894 0.0031629656
## GO:0038201 GO:0038201      TOR complex       1/7 12/19894 0.0042153801
##              p.adjust     qvalue geneID Count
## GO:0070557 0.02531518 0.01628462 CDKN1A     1
## GO:0031931 0.02531518 0.01628462   MTOR     1
## GO:0097441 0.02531518 0.01628462  MAPK8     1
## GO:0031932 0.02846669 0.01831191   MTOR     1
## GO:0038201 0.03035074 0.01952387   MTOR     1
##                    ID                                        Description
## GO:0106310 GO:0106310                     protein serine kinase activity
## GO:0004674 GO:0004674           protein serine/threonine kinase activity
## GO:0004707 GO:0004707                                MAP kinase activity
## GO:0070064 GO:0070064                        proline-rich region binding
## GO:0042826 GO:0042826                        histone deacetylase binding
## GO:0030291 GO:0030291 protein serine/threonine kinase inhibitor activity
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue
## GO:0106310      5/16 363/18522 1.028418e-05 0.001244385 0.0004330180
## GO:0004674      5/16 427/18522 2.252414e-05 0.001362710 0.0004741923
## GO:0004707      2/16  16/18522 8.336346e-05 0.002856537 0.0009940104
## GO:0070064      2/16  17/18522 9.443099e-05 0.002856537 0.0009940104
## GO:0042826      3/16 128/18522 1.690349e-04 0.004090645 0.0014234520
## GO:0030291      2/16  37/18522 4.577980e-04 0.009232259 0.0032126172
##                               geneID Count
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1     5
## GO:0004707               MAPK8/MAPK1     2
## GO:0070064                CCND1/YAP1     2
## GO:0042826        HSPA1A/MAPK8/CCND1     3
## GO:0030291               AKT1/CDKN1A     2
##                    ID                                  Description GeneRatio
## GO:0062197 GO:0062197         cellular response to chemical stress      7/16
## GO:0009408 GO:0009408                             response to heat      5/16
## GO:0034599 GO:0034599        cellular response to oxidative stress      6/16
## GO:0034198 GO:0034198   cellular response to amino acid starvation      4/16
## GO:1990928 GO:1990928            response to amino acid starvation      4/16
## GO:0034614 GO:0034614 cellular response to reactive oxygen species      5/16
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0062197 311/18888 3.090160e-09 5.185288e-06 1.876866e-06
## GO:0009408 104/18888 1.911902e-08 1.604086e-05 5.806146e-06
## GO:0034599 248/18888 3.459920e-08 1.935249e-05 7.004821e-06
## GO:0034198  51/18888 8.376414e-08 3.337785e-05 1.208144e-05
## GO:1990928  54/18888 1.058426e-07 3.337785e-05 1.208144e-05
## GO:0034614 151/18888 1.243248e-07 3.337785e-05 1.208144e-05
##                                            geneID Count
## GO:0062197 HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/MAPK1     7
## GO:0009408            HSPA1A/AKT1/MTOR/CDKN1A/ATM     5
## GO:0034599      HSPA1A/AKT1/MAPK8/FOXO3/ATM/MAPK1     6
## GO:0034198                MTOR/MAPK8/CDKN1A/MAPK1     4
## GO:1990928                MTOR/MAPK8/CDKN1A/MAPK1     4
## GO:0034614             AKT1/MAPK8/FOXO3/ATM/MAPK1     5
##                    ID                                        Description
## GO:0005826 GO:0005826                        actomyosin contractile ring
## GO:0070938 GO:0070938                                   contractile ring
## GO:0005819 GO:0005819                                            spindle
## GO:0008180 GO:0008180                                   COP9 signalosome
## GO:0005741 GO:0005741                       mitochondrial outer membrane
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0005826      2/16   4/19894 3.635235e-06 0.0003635235 0.0001913281
## GO:0070938      2/16  10/19894 2.718760e-05 0.0013593802 0.0007154633
## GO:0005819      4/16 433/19894 3.272457e-04 0.0094003057 0.0049475293
## GO:0008180      2/16  36/19894 3.760122e-04 0.0094003057 0.0049475293
## GO:0005741      3/16 219/19894 6.628567e-04 0.0121604395 0.0064002313
## GO:0000307      2/16  56/19894 9.105620e-04 0.0121604395 0.0064002313
##                         geneID Count
## GO:0005826           MYH9/ANLN     2
## GO:0070938           MYH9/ANLN     2
## GO:0005819 AKT1/MYH9/ATM/MAPK1     4
## GO:0008180         HSPA1A/MYH9     2
## GO:0005741    MTOR/FOXO3/CASP8     3
## GO:0000307        CDKN1A/CCND1     2
##                    ID
## GO:0120283 GO:0120283
## GO:0003713 GO:0003713
## GO:0030374 GO:0030374
## GO:0061629 GO:0061629
## GO:0140297 GO:0140297
## GO:0016922 GO:0016922
##                                                                    Description
## GO:0120283                             protein serine/threonine kinase binding
## GO:0003713                                  transcription coactivator activity
## GO:0030374                               nuclear receptor coactivator activity
## GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
## GO:0140297                            DNA-binding transcription factor binding
## GO:0016922                                            nuclear receptor binding
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0120283       2/7   7/18522 2.568771e-06 0.0001592638 6.489527e-05
## GO:0003713       3/7 271/18522 1.038059e-04 0.0032179819 1.311232e-03
## GO:0030374       2/7  55/18522 1.800853e-04 0.0032316692 1.316809e-03
## GO:0061629       3/7 343/18522 2.084948e-04 0.0032316692 1.316809e-03
## GO:0140297       3/7 478/18522 5.532853e-04 0.0068607374 2.795547e-03
## GO:0016922       2/7 136/18522 1.097114e-03 0.0100388592 4.090537e-03
##                       geneID Count
## GO:0120283        XIAP/MAPK8     2
## GO:0003713 ETS1/ARID1A/NCOA3     3
## GO:0030374        ETS1/NCOA3     2
## GO:0061629 ETS1/ARID1A/NCOA3     3
## GO:0140297 ETS1/ARID1A/NCOA3     3
## GO:0016922      ARID1A/NCOA3     2
##                    ID
## GO:1902459 GO:1902459
## GO:0030522 GO:0030522
## GO:2000036 GO:2000036
## GO:0039531 GO:0039531
## GO:1902528 GO:1902528
## GO:1902530 GO:1902530
##                                                                         Description
## GO:1902459                  positive regulation of stem cell population maintenance
## GO:0030522                                 intracellular receptor signaling pathway
## GO:2000036                           regulation of stem cell population maintenance
## GO:0039531 regulation of cytoplasmic pattern recognition receptor signaling pathway
## GO:1902528                          regulation of protein linear polyubiquitination
## GO:1902530                 positive regulation of protein linear polyubiquitination
##            GeneRatio   BgRatio       pvalue   p.adjust     qvalue
## GO:1902459       2/7  48/18888 0.0001317291 0.04033235 0.01854731
## GO:0030522       3/7 369/18888 0.0002441855 0.04033235 0.01854731
## GO:2000036       2/7  73/18888 0.0003055481 0.04033235 0.01854731
## GO:0039531       2/7 108/18888 0.0006676434 0.04192472 0.01927958
## GO:1902528       1/7   2/18888 0.0007410936 0.04192472 0.01927958
## GO:1902530       1/7   2/18888 0.0007410936 0.04192472 0.01927958
##                       geneID Count
## GO:1902459      ARID1A/NCOA3     2
## GO:0030522 XIAP/MAPK8/ARID1A     3
## GO:2000036      ARID1A/NCOA3     2
## GO:0039531        XIAP/MAPK8     2
## GO:1902528              XIAP     1
## GO:1902530              XIAP     1
##                    ID     Description GeneRatio  BgRatio      pvalue   p.adjust
## GO:0097441 GO:0097441  basal dendrite       1/7  6/19894 0.002109598 0.01460451
## GO:0140092 GO:0140092    bBAF complex       1/7 10/19894 0.003513876 0.01460451
## GO:0035060 GO:0035060  brahma complex       1/7 14/19894 0.004916460 0.01460451
## GO:0071564 GO:0071564   npBAF complex       1/7 14/19894 0.004916460 0.01460451
## GO:0071565 GO:0071565    nBAF complex       1/7 16/19894 0.005617118 0.01460451
## GO:0016514 GO:0016514 SWI/SNF complex       1/7 30/19894 0.010509889 0.02277143
##                 qvalue geneID Count
## GO:0097441 0.007095307  MAPK8     1
## GO:0140092 0.007095307 ARID1A     1
## GO:0035060 0.007095307 ARID1A     1
## GO:0071564 0.007095307 ARID1A     1
## GO:0071565 0.007095307 ARID1A     1
## GO:0016514 0.011063041 ARID1A     1
##                    ID                                        Description
## GO:0106310 GO:0106310                     protein serine kinase activity
## GO:0004674 GO:0004674           protein serine/threonine kinase activity
## GO:0030291 GO:0030291 protein serine/threonine kinase inhibitor activity
## GO:0003925 GO:0003925                                 G protein activity
## GO:0004860 GO:0004860                  protein kinase inhibitor activity
## GO:0019003 GO:0019003                                        GDP binding
##            GeneRatio   BgRatio       pvalue   p.adjust      qvalue
## GO:0106310      4/14 363/18522 0.0001243240 0.01398998 0.004044545
## GO:0004674      4/14 427/18522 0.0002320529 0.01398998 0.004044545
## GO:0030291      2/14  37/18522 0.0003480386 0.01398998 0.004044545
## GO:0003925      2/14  45/18522 0.0005155705 0.01398998 0.004044545
## GO:0004860      2/14  73/18522 0.0013521609 0.01398998 0.004044545
## GO:0019003      2/14  75/18522 0.0014265635 0.01398998 0.004044545
##                         geneID Count
## GO:0106310 AKT1/MTOR/MAPK8/ATM     4
## GO:0004674 AKT1/MTOR/MAPK8/ATM     4
## GO:0030291         AKT1/CDKN1A     2
## GO:0003925           KRAS/NRAS     2
## GO:0004860         AKT1/CDKN1A     2
## GO:0019003           KRAS/NRAS     2
##                    ID                                      Description
## GO:0010632 GO:0010632          regulation of epithelial cell migration
## GO:0010634 GO:0010634 positive regulation of epithelial cell migration
## GO:0010631 GO:0010631                        epithelial cell migration
## GO:0090132 GO:0090132                             epithelium migration
## GO:0090130 GO:0090130                                 tissue migration
## GO:0009408 GO:0009408                                 response to heat
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0010632      7/14 298/18888 7.082024e-10 1.117543e-06 3.682652e-07
## GO:0010634      6/14 177/18888 1.755369e-09 1.279107e-06 4.215054e-07
## GO:0010631      7/14 375/18888 3.501293e-09 1.279107e-06 4.215054e-07
## GO:0090132      7/14 378/18888 3.700139e-09 1.279107e-06 4.215054e-07
## GO:0090130      7/14 383/18888 4.052937e-09 1.279107e-06 4.215054e-07
## GO:0009408      5/14 104/18888 8.839902e-09 2.324894e-06 7.661248e-07
##                                           geneID Count
## GO:0010632 AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2     7
## GO:0010634      AKT1/MTOR/PTK2/ETS1/STAT5A/ITGA2     6
## GO:0010631 AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2     7
## GO:0090132 AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2     7
## GO:0090130 AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2     7
## GO:0009408           HSPA1A/AKT1/MTOR/ATM/CDKN1A     5
##                    ID                   Description GeneRatio   BgRatio
## GO:0005925 GO:0005925                focal adhesion      4/14 421/19894
## GO:0030055 GO:0030055       cell-substrate junction      4/14 431/19894
## GO:0070557 GO:0070557              PCNA-p21 complex      1/14   2/19894
## GO:0034666 GO:0034666 integrin alpha2-beta1 complex      1/14   3/19894
## GO:0016605 GO:0016605                      PML body      2/14 108/19894
## GO:0031931 GO:0031931                 TORC1 complex      1/14   6/19894
##                  pvalue    p.adjust      qvalue                 geneID Count
## GO:0005925 0.0001672496 0.006680633 0.003949617 HSPA1A/KRAS/PTK2/ITGA2     4
## GO:0030055 0.0001830310 0.006680633 0.003949617 HSPA1A/KRAS/PTK2/ITGA2     4
## GO:0070557 0.0014069997 0.034236992 0.020241048                 CDKN1A     1
## GO:0034666 0.0021098099 0.035870172 0.021206591                  ITGA2     1
## GO:0016605 0.0025463690 0.035870172 0.021206591              MTOR/PTEN     2
## GO:0031931 0.0042154859 0.035870172 0.021206591                   MTOR     1
##                    ID
## GO:0070064 GO:0070064
## GO:0016538 GO:0016538
## GO:0004677 GO:0004677
## GO:0035979 GO:0035979
## GO:0030295 GO:0030295
## GO:0034246 GO:0034246
##                                                                    Description
## GO:0070064                                         proline-rich region binding
## GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity
## GO:0004677                               DNA-dependent protein kinase activity
## GO:0035979                                    histone H2AXS139 kinase activity
## GO:0030295                                   protein kinase activator activity
## GO:0034246                         mitochondrial transcription factor activity
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue
## GO:0070064      2/10  17/18522 3.552653e-05 0.002415804 0.0007479269
## GO:0016538      2/10  50/18522 3.169725e-04 0.010777065 0.0033365527
## GO:0004677      1/10   3/18522 1.618909e-03 0.017762122 0.0054991088
## GO:0035979      1/10   3/18522 1.618909e-03 0.017762122 0.0054991088
## GO:0030295      2/10 129/18522 2.088189e-03 0.017762122 0.0054991088
## GO:0034246      1/10   4/18522 2.158020e-03 0.017762122 0.0054991088
##                  geneID Count
## GO:0070064   CCND1/YAP1     2
## GO:0016538 CDKN1A/CCND1     2
## GO:0004677          ATM     1
## GO:0035979          ATM     1
## GO:0030295 CDKN1A/CCND1     2
## GO:0034246        FOXO3     1
##                    ID                                   Description GeneRatio
## GO:0071480 GO:0071480          cellular response to gamma radiation      3/10
## GO:0031571 GO:0031571    mitotic G1 DNA damage checkpoint signaling      3/10
## GO:0044819 GO:0044819  mitotic G1/S transition checkpoint signaling      3/10
## GO:0001701 GO:0001701                in utero embryonic development      5/10
## GO:0042770 GO:0042770 signal transduction in response to DNA damage      4/10
## GO:0010332 GO:0010332                   response to gamma radiation      3/10
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0071480  27/18888 3.105065e-07 0.0001393819 4.729419e-05
## GO:0031571  30/18888 4.306340e-07 0.0001393819 4.729419e-05
## GO:0044819  30/18888 4.306340e-07 0.0001393819 4.729419e-05
## GO:0001701 401/18888 9.711876e-07 0.0002357558 7.999519e-05
## GO:0042770 188/18888 1.905112e-06 0.0003699728 1.255369e-04
## GO:0010332  52/18888 2.329784e-06 0.0003770367 1.279338e-04
##                                  geneID Count
## GO:0071480              CDKN1A/ATM/YAP1     3
## GO:0031571             CDKN1A/ATM/CCND1     3
## GO:0044819             CDKN1A/ATM/CCND1     3
## GO:0001701 MYH9/CDKN1A/CASP8/YAP1/MAPK1     5
## GO:0042770       CDKN1A/FOXO3/ATM/CCND1     4
## GO:0010332              CDKN1A/ATM/YAP1     3
##                    ID                                        Description
## GO:0005826 GO:0005826                        actomyosin contractile ring
## GO:0070938 GO:0070938                                   contractile ring
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0030864 GO:0030864                        cortical actin cytoskeleton
## GO:0032153 GO:0032153                                 cell division site
## GO:0017053 GO:0017053                    transcription repressor complex
##            GeneRatio  BgRatio       pvalue     p.adjust       qvalue
## GO:0005826      2/10  4/19894 1.363762e-06 0.0001131922 4.880831e-05
## GO:0070938      2/10 10/19894 1.021177e-05 0.0004237884 1.827369e-04
## GO:0000307      2/10 56/19894 3.451847e-04 0.0090216453 3.890120e-03
## GO:0030864      2/10 72/19894 5.704635e-04 0.0090216453 3.890120e-03
## GO:0032153      2/10 73/19894 5.863756e-04 0.0090216453 3.890120e-03
## GO:0017053      2/10 77/19894 6.521671e-04 0.0090216453 3.890120e-03
##                  geneID Count
## GO:0005826    MYH9/ANLN     2
## GO:0070938    MYH9/ANLN     2
## GO:0000307 CDKN1A/CCND1     2
## GO:0030864    MYH9/ANLN     2
## GO:0032153    MYH9/ANLN     2
## GO:0017053  FOXO3/CCND1     2
##                    ID
## GO:0120283 GO:0120283
## GO:0003713 GO:0003713
## GO:0030374 GO:0030374
## GO:0061629 GO:0061629
## GO:0140297 GO:0140297
## GO:0016922 GO:0016922
##                                                                    Description
## GO:0120283                             protein serine/threonine kinase binding
## GO:0003713                                  transcription coactivator activity
## GO:0030374                               nuclear receptor coactivator activity
## GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
## GO:0140297                            DNA-binding transcription factor binding
## GO:0016922                                            nuclear receptor binding
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0120283       2/7   7/18522 2.568771e-06 0.0001592638 6.489527e-05
## GO:0003713       3/7 271/18522 1.038059e-04 0.0032179819 1.311232e-03
## GO:0030374       2/7  55/18522 1.800853e-04 0.0032316692 1.316809e-03
## GO:0061629       3/7 343/18522 2.084948e-04 0.0032316692 1.316809e-03
## GO:0140297       3/7 478/18522 5.532853e-04 0.0068607374 2.795547e-03
## GO:0016922       2/7 136/18522 1.097114e-03 0.0100388592 4.090537e-03
##                       geneID Count
## GO:0120283        XIAP/MAPK8     2
## GO:0003713 ETS1/ARID1A/NCOA3     3
## GO:0030374        ETS1/NCOA3     2
## GO:0061629 ETS1/ARID1A/NCOA3     3
## GO:0140297 ETS1/ARID1A/NCOA3     3
## GO:0016922      ARID1A/NCOA3     2
##                    ID
## GO:1902459 GO:1902459
## GO:0030522 GO:0030522
## GO:2000036 GO:2000036
## GO:0039531 GO:0039531
## GO:1902528 GO:1902528
## GO:1902530 GO:1902530
##                                                                         Description
## GO:1902459                  positive regulation of stem cell population maintenance
## GO:0030522                                 intracellular receptor signaling pathway
## GO:2000036                           regulation of stem cell population maintenance
## GO:0039531 regulation of cytoplasmic pattern recognition receptor signaling pathway
## GO:1902528                          regulation of protein linear polyubiquitination
## GO:1902530                 positive regulation of protein linear polyubiquitination
##            GeneRatio   BgRatio       pvalue   p.adjust     qvalue
## GO:1902459       2/7  48/18888 0.0001317291 0.04033235 0.01854731
## GO:0030522       3/7 369/18888 0.0002441855 0.04033235 0.01854731
## GO:2000036       2/7  73/18888 0.0003055481 0.04033235 0.01854731
## GO:0039531       2/7 108/18888 0.0006676434 0.04192472 0.01927958
## GO:1902528       1/7   2/18888 0.0007410936 0.04192472 0.01927958
## GO:1902530       1/7   2/18888 0.0007410936 0.04192472 0.01927958
##                       geneID Count
## GO:1902459      ARID1A/NCOA3     2
## GO:0030522 XIAP/MAPK8/ARID1A     3
## GO:2000036      ARID1A/NCOA3     2
## GO:0039531        XIAP/MAPK8     2
## GO:1902528              XIAP     1
## GO:1902530              XIAP     1
##                    ID     Description GeneRatio  BgRatio      pvalue   p.adjust
## GO:0097441 GO:0097441  basal dendrite       1/7  6/19894 0.002109598 0.01460451
## GO:0140092 GO:0140092    bBAF complex       1/7 10/19894 0.003513876 0.01460451
## GO:0035060 GO:0035060  brahma complex       1/7 14/19894 0.004916460 0.01460451
## GO:0071564 GO:0071564   npBAF complex       1/7 14/19894 0.004916460 0.01460451
## GO:0071565 GO:0071565    nBAF complex       1/7 16/19894 0.005617118 0.01460451
## GO:0016514 GO:0016514 SWI/SNF complex       1/7 30/19894 0.010509889 0.02277143
##                 qvalue geneID Count
## GO:0097441 0.007095307  MAPK8     1
## GO:0140092 0.007095307 ARID1A     1
## GO:0035060 0.007095307 ARID1A     1
## GO:0071564 0.007095307 ARID1A     1
## GO:0071565 0.007095307 ARID1A     1
## GO:0016514 0.011063041 ARID1A     1
##                    ID
## GO:0120283 GO:0120283
## GO:0003713 GO:0003713
## GO:0030374 GO:0030374
## GO:0061629 GO:0061629
## GO:0140297 GO:0140297
## GO:0016922 GO:0016922
##                                                                    Description
## GO:0120283                             protein serine/threonine kinase binding
## GO:0003713                                  transcription coactivator activity
## GO:0030374                               nuclear receptor coactivator activity
## GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
## GO:0140297                            DNA-binding transcription factor binding
## GO:0016922                                            nuclear receptor binding
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0120283       2/7   7/18522 2.568771e-06 0.0001592638 6.489527e-05
## GO:0003713       3/7 271/18522 1.038059e-04 0.0032179819 1.311232e-03
## GO:0030374       2/7  55/18522 1.800853e-04 0.0032316692 1.316809e-03
## GO:0061629       3/7 343/18522 2.084948e-04 0.0032316692 1.316809e-03
## GO:0140297       3/7 478/18522 5.532853e-04 0.0068607374 2.795547e-03
## GO:0016922       2/7 136/18522 1.097114e-03 0.0100388592 4.090537e-03
##                       geneID Count
## GO:0120283        XIAP/MAPK8     2
## GO:0003713 ETS1/ARID1A/NCOA3     3
## GO:0030374        ETS1/NCOA3     2
## GO:0061629 ETS1/ARID1A/NCOA3     3
## GO:0140297 ETS1/ARID1A/NCOA3     3
## GO:0016922      ARID1A/NCOA3     2
##                    ID
## GO:1902459 GO:1902459
## GO:0030522 GO:0030522
## GO:2000036 GO:2000036
## GO:0039531 GO:0039531
## GO:1902528 GO:1902528
## GO:1902530 GO:1902530
##                                                                         Description
## GO:1902459                  positive regulation of stem cell population maintenance
## GO:0030522                                 intracellular receptor signaling pathway
## GO:2000036                           regulation of stem cell population maintenance
## GO:0039531 regulation of cytoplasmic pattern recognition receptor signaling pathway
## GO:1902528                          regulation of protein linear polyubiquitination
## GO:1902530                 positive regulation of protein linear polyubiquitination
##            GeneRatio   BgRatio       pvalue   p.adjust     qvalue
## GO:1902459       2/7  48/18888 0.0001317291 0.04033235 0.01854731
## GO:0030522       3/7 369/18888 0.0002441855 0.04033235 0.01854731
## GO:2000036       2/7  73/18888 0.0003055481 0.04033235 0.01854731
## GO:0039531       2/7 108/18888 0.0006676434 0.04192472 0.01927958
## GO:1902528       1/7   2/18888 0.0007410936 0.04192472 0.01927958
## GO:1902530       1/7   2/18888 0.0007410936 0.04192472 0.01927958
##                       geneID Count
## GO:1902459      ARID1A/NCOA3     2
## GO:0030522 XIAP/MAPK8/ARID1A     3
## GO:2000036      ARID1A/NCOA3     2
## GO:0039531        XIAP/MAPK8     2
## GO:1902528              XIAP     1
## GO:1902530              XIAP     1
##                    ID     Description GeneRatio  BgRatio      pvalue   p.adjust
## GO:0097441 GO:0097441  basal dendrite       1/7  6/19894 0.002109598 0.01460451
## GO:0140092 GO:0140092    bBAF complex       1/7 10/19894 0.003513876 0.01460451
## GO:0035060 GO:0035060  brahma complex       1/7 14/19894 0.004916460 0.01460451
## GO:0071564 GO:0071564   npBAF complex       1/7 14/19894 0.004916460 0.01460451
## GO:0071565 GO:0071565    nBAF complex       1/7 16/19894 0.005617118 0.01460451
## GO:0016514 GO:0016514 SWI/SNF complex       1/7 30/19894 0.010509889 0.02277143
##                 qvalue geneID Count
## GO:0097441 0.007095307  MAPK8     1
## GO:0140092 0.007095307 ARID1A     1
## GO:0035060 0.007095307 ARID1A     1
## GO:0071564 0.007095307 ARID1A     1
## GO:0071565 0.007095307 ARID1A     1
## GO:0016514 0.011063041 ARID1A     1
##                    ID                                 Description GeneRatio
## GO:0043394 GO:0043394                        proteoglycan binding       1/1
## GO:0016504 GO:0016504                peptidase activator activity       1/1
## GO:0005518 GO:0005518                            collagen binding       1/1
## GO:0002020 GO:0002020                            protease binding       1/1
## GO:0005178 GO:0005178                            integrin binding       1/1
## GO:0005201 GO:0005201 extracellular matrix structural constituent       1/1
##              BgRatio      pvalue   p.adjust qvalue geneID Count
## GO:0043394  36/18522 0.001943635 0.01223770     NA    FN1     1
## GO:0016504  55/18522 0.002969442 0.01223770     NA    FN1     1
## GO:0005518  68/18522 0.003671310 0.01223770     NA    FN1     1
## GO:0002020 140/18522 0.007558579 0.01342033     NA    FN1     1
## GO:0005178 157/18522 0.008476406 0.01342033     NA    FN1     1
## GO:0005201 166/18522 0.008962315 0.01342033     NA    FN1     1
##                    ID
## GO:1904235 GO:1904235
## GO:1904237 GO:1904237
## GO:0006931 GO:0006931
## GO:0150102 GO:0150102
## GO:0007161 GO:0007161
## GO:1901166 GO:1901166
##                                                                                        Description
## GO:1904235          regulation of substrate-dependent cell migration, cell attachment to substrate
## GO:1904237 positive regulation of substrate-dependent cell migration, cell attachment to substrate
## GO:0006931                        substrate-dependent cell migration, cell attachment to substrate
## GO:0150102                                              negative regulation of monocyte activation
## GO:0007161                                                calcium-independent cell-matrix adhesion
## GO:1901166            neural crest cell migration involved in autonomic nervous system development
##            GeneRatio BgRatio       pvalue    p.adjust qvalue geneID Count
## GO:1904235       1/1 2/18888 0.0001058873 0.003256036     NA    FN1     1
## GO:1904237       1/1 2/18888 0.0001058873 0.003256036     NA    FN1     1
## GO:0006931       1/1 3/18888 0.0001588310 0.003256036     NA    FN1     1
## GO:0150102       1/1 3/18888 0.0001588310 0.003256036     NA    FN1     1
## GO:0007161       1/1 4/18888 0.0002117747 0.003473105     NA    FN1     1
## GO:1901166       1/1 6/18888 0.0003176620 0.004341381     NA    FN1     1
##                    ID                                          Description
## GO:0005577 GO:0005577                                   fibrinogen complex
## GO:0031093 GO:0031093                         platelet alpha granule lumen
## GO:0031091 GO:0031091                               platelet alpha granule
## GO:0005604 GO:0005604                                    basement membrane
## GO:0005793 GO:0005793 endoplasmic reticulum-Golgi intermediate compartment
## GO:0072562 GO:0072562                                  blood microparticle
##            GeneRatio   BgRatio       pvalue    p.adjust qvalue geneID Count
## GO:0005577       1/1   8/19894 0.0004021313 0.005227707     NA    FN1     1
## GO:0031093       1/1  67/19894 0.0033678496 0.015029657     NA    FN1     1
## GO:0031091       1/1  91/19894 0.0045742435 0.015029657     NA    FN1     1
## GO:0005604       1/1  92/19894 0.0046245099 0.015029657     NA    FN1     1
## GO:0005793       1/1 133/19894 0.0066854328 0.015683121     NA    FN1     1
## GO:0072562       1/1 144/19894 0.0072383633 0.015683121     NA    FN1     1
##                    ID
## GO:0070064 GO:0070064
## GO:0016538 GO:0016538
## GO:0004677 GO:0004677
## GO:0035979 GO:0035979
## GO:0030295 GO:0030295
## GO:0034246 GO:0034246
##                                                                    Description
## GO:0070064                                         proline-rich region binding
## GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity
## GO:0004677                               DNA-dependent protein kinase activity
## GO:0035979                                    histone H2AXS139 kinase activity
## GO:0030295                                   protein kinase activator activity
## GO:0034246                         mitochondrial transcription factor activity
##            GeneRatio   BgRatio       pvalue    p.adjust       qvalue
## GO:0070064      2/10  17/18522 3.552653e-05 0.002415804 0.0007479269
## GO:0016538      2/10  50/18522 3.169725e-04 0.010777065 0.0033365527
## GO:0004677      1/10   3/18522 1.618909e-03 0.017762122 0.0054991088
## GO:0035979      1/10   3/18522 1.618909e-03 0.017762122 0.0054991088
## GO:0030295      2/10 129/18522 2.088189e-03 0.017762122 0.0054991088
## GO:0034246      1/10   4/18522 2.158020e-03 0.017762122 0.0054991088
##                  geneID Count
## GO:0070064   CCND1/YAP1     2
## GO:0016538 CDKN1A/CCND1     2
## GO:0004677          ATM     1
## GO:0035979          ATM     1
## GO:0030295 CDKN1A/CCND1     2
## GO:0034246        FOXO3     1
##                    ID                                   Description GeneRatio
## GO:0071480 GO:0071480          cellular response to gamma radiation      3/10
## GO:0031571 GO:0031571    mitotic G1 DNA damage checkpoint signaling      3/10
## GO:0044819 GO:0044819  mitotic G1/S transition checkpoint signaling      3/10
## GO:0001701 GO:0001701                in utero embryonic development      5/10
## GO:0042770 GO:0042770 signal transduction in response to DNA damage      4/10
## GO:0010332 GO:0010332                   response to gamma radiation      3/10
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0071480  27/18888 3.105065e-07 0.0001393819 4.729419e-05
## GO:0031571  30/18888 4.306340e-07 0.0001393819 4.729419e-05
## GO:0044819  30/18888 4.306340e-07 0.0001393819 4.729419e-05
## GO:0001701 401/18888 9.711876e-07 0.0002357558 7.999519e-05
## GO:0042770 188/18888 1.905112e-06 0.0003699728 1.255369e-04
## GO:0010332  52/18888 2.329784e-06 0.0003770367 1.279338e-04
##                                  geneID Count
## GO:0071480              CDKN1A/ATM/YAP1     3
## GO:0031571             CDKN1A/ATM/CCND1     3
## GO:0044819             CDKN1A/ATM/CCND1     3
## GO:0001701 MYH9/CDKN1A/CASP8/YAP1/MAPK1     5
## GO:0042770       CDKN1A/FOXO3/ATM/CCND1     4
## GO:0010332              CDKN1A/ATM/YAP1     3
##                    ID                                        Description
## GO:0005826 GO:0005826                        actomyosin contractile ring
## GO:0070938 GO:0070938                                   contractile ring
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0030864 GO:0030864                        cortical actin cytoskeleton
## GO:0032153 GO:0032153                                 cell division site
## GO:0017053 GO:0017053                    transcription repressor complex
##            GeneRatio  BgRatio       pvalue     p.adjust       qvalue
## GO:0005826      2/10  4/19894 1.363762e-06 0.0001131922 4.880831e-05
## GO:0070938      2/10 10/19894 1.021177e-05 0.0004237884 1.827369e-04
## GO:0000307      2/10 56/19894 3.451847e-04 0.0090216453 3.890120e-03
## GO:0030864      2/10 72/19894 5.704635e-04 0.0090216453 3.890120e-03
## GO:0032153      2/10 73/19894 5.863756e-04 0.0090216453 3.890120e-03
## GO:0017053      2/10 77/19894 6.521671e-04 0.0090216453 3.890120e-03
##                  geneID Count
## GO:0005826    MYH9/ANLN     2
## GO:0070938    MYH9/ANLN     2
## GO:0000307 CDKN1A/CCND1     2
## GO:0030864    MYH9/ANLN     2
## GO:0032153    MYH9/ANLN     2
## GO:0017053  FOXO3/CCND1     2
##                    ID
## GO:0004345 GO:0004345
## GO:0005536 GO:0005536
## GO:0050661 GO:0050661
## GO:0048029 GO:0048029
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
##                                                                                      Description
## GO:0004345                                            glucose-6-phosphate dehydrogenase activity
## GO:0005536                                                                       glucose binding
## GO:0050661                                                                          NADP binding
## GO:0048029                                                                monosaccharide binding
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614                              oxidoreductase activity, acting on CH-OH group of donors
##            GeneRatio   BgRatio       pvalue     p.adjust qvalue geneID Count
## GO:0004345       1/1   2/18522 0.0001079797 0.0007558579     NA   G6PD     1
## GO:0005536       1/1  11/18522 0.0005938883 0.0020786092     NA   G6PD     1
## GO:0050661       1/1  53/18522 0.0028614620 0.0066767448     NA   G6PD     1
## GO:0048029       1/1  74/18522 0.0039952489 0.0069916856     NA   G6PD     1
## GO:0016616       1/1 125/18522 0.0067487312 0.0085034014     NA   G6PD     1
## GO:0016614       1/1 135/18522 0.0072886297 0.0085034014     NA   G6PD     1
##                    ID
## GO:0010731 GO:0010731
## GO:0010732 GO:0010732
## GO:0010734 GO:0010734
## GO:0019322 GO:0019322
## GO:1904879 GO:1904879
## GO:0009051 GO:0009051
##                                                                                                  Description
## GO:0010731                                                                         protein glutathionylation
## GO:0010732                                                           regulation of protein glutathionylation
## GO:0010734                                                  negative regulation of protein glutathionylation
## GO:0019322                                                                      pentose biosynthetic process
## GO:1904879 positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel
## GO:0009051                                                         pentose-phosphate shunt, oxidative branch
##            GeneRatio BgRatio       pvalue    p.adjust qvalue geneID Count
## GO:0010731       1/1 2/18888 0.0001058873 0.003388395     NA   G6PD     1
## GO:0010732       1/1 2/18888 0.0001058873 0.003388395     NA   G6PD     1
## GO:0010734       1/1 2/18888 0.0001058873 0.003388395     NA   G6PD     1
## GO:0019322       1/1 2/18888 0.0001058873 0.003388395     NA   G6PD     1
## GO:1904879       1/1 3/18888 0.0001588310 0.003872451     NA   G6PD     1
## GO:0009051       1/1 4/18888 0.0002117747 0.003872451     NA   G6PD     1
##                    ID                         Description GeneRatio   BgRatio
## GO:0034451 GO:0034451                centriolar satellite       1/1 126/19894
## GO:0009898 GO:0009898 cytoplasmic side of plasma membrane       1/1 161/19894
## GO:0098562 GO:0098562        cytoplasmic side of membrane       1/1 199/19894
##                 pvalue   p.adjust qvalue geneID Count
## GO:0034451 0.006333568 0.01000302     NA   G6PD     1
## GO:0009898 0.008092892 0.01000302     NA   G6PD     1
## GO:0098562 0.010003016 0.01000302     NA   G6PD     1
##                    ID
## GO:0004365 GO:0004365
## GO:0043891 GO:0043891
## GO:0019828 GO:0019828
## GO:0016769 GO:0016769
## GO:0097718 GO:0097718
## GO:0016620 GO:0016620
##                                                                                                Description
## GO:0004365                      glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
## GO:0043891                   glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity
## GO:0019828                                                  aspartic-type endopeptidase inhibitor activity
## GO:0016769                                           transferase activity, transferring nitrogenous groups
## GO:0097718                                                              disordered domain specific binding
## GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
##            GeneRatio  BgRatio       pvalue     p.adjust qvalue geneID Count
## GO:0004365       1/1  2/18522 0.0001079797 0.0008638376     NA  GAPDH     1
## GO:0043891       1/1  2/18522 0.0001079797 0.0008638376     NA  GAPDH     1
## GO:0019828       1/1  8/18522 0.0004319188 0.0023035669     NA  GAPDH     1
## GO:0016769       1/1 26/18522 0.0014037361 0.0050870436     NA  GAPDH     1
## GO:0097718       1/1 32/18522 0.0017276752 0.0050870436     NA  GAPDH     1
## GO:0016620       1/1 39/18522 0.0021056041 0.0050870436     NA  GAPDH     1
##                    ID                             Description GeneRatio
## GO:0035606 GO:0035606 peptidyl-cysteine S-trans-nitrosylation       1/1
## GO:0017014 GO:0017014                   protein nitrosylation       1/1
## GO:0018119 GO:0018119       peptidyl-cysteine S-nitrosylation       1/1
## GO:0051873 GO:0051873       killing by host of symbiont cells       1/1
## GO:0018198 GO:0018198          peptidyl-cysteine modification       1/1
## GO:0050832 GO:0050832              defense response to fungus       1/1
##             BgRatio       pvalue    p.adjust qvalue geneID Count
## GO:0035606  2/18888 0.0001058873 0.008259212     NA  GAPDH     1
## GO:0017014 16/18888 0.0008470987 0.016071980     NA  GAPDH     1
## GO:0018119 16/18888 0.0008470987 0.016071980     NA  GAPDH     1
## GO:0051873 28/18888 0.0014824227 0.016071980     NA  GAPDH     1
## GO:0018198 45/18888 0.0023824651 0.016071980     NA  GAPDH     1
## GO:0050832 56/18888 0.0029648454 0.016071980     NA  GAPDH     1
##                    ID      Description GeneRatio   BgRatio       pvalue
## GO:0097452 GO:0097452     GAIT complex       1/1   4/19894 0.0002010656
## GO:0005811 GO:0005811    lipid droplet       1/1 104/19894 0.0052277068
## GO:0031965 GO:0031965 nuclear membrane       1/1 313/19894 0.0157333870
## GO:0005635 GO:0005635 nuclear envelope       1/1 498/19894 0.0250326732
##                p.adjust qvalue geneID Count
## GO:0097452 0.0008042626     NA  GAPDH     1
## GO:0005811 0.0104554137     NA  GAPDH     1
## GO:0031965 0.0209778493     NA  GAPDH     1
## GO:0005635 0.0250326732     NA  GAPDH     1
##                    ID                        Description GeneRatio  BgRatio
## GO:0045294 GO:0045294              alpha-catenin binding       1/1 10/18522
## GO:0070411 GO:0070411                     I-SMAD binding       1/1 16/18522
## GO:0097718 GO:0097718 disordered domain specific binding       1/1 32/18522
## GO:0030331 GO:0030331  nuclear estrogen receptor binding       1/1 39/18522
## GO:0001222 GO:0001222  transcription corepressor binding       1/1 47/18522
## GO:0046332 GO:0046332                       SMAD binding       1/1 78/18522
##                  pvalue    p.adjust qvalue geneID Count
## GO:0045294 0.0005398985 0.007342620     NA CTNNB1     1
## GO:0070411 0.0008638376 0.007342620     NA CTNNB1     1
## GO:0097718 0.0017276752 0.008627578     NA CTNNB1     1
## GO:0030331 0.0021056041 0.008627578     NA CTNNB1     1
## GO:0001222 0.0025375229 0.008627578     NA CTNNB1     1
## GO:0046332 0.0042112083 0.011931757     NA CTNNB1     1
##                    ID
## GO:0003340 GO:0003340
## GO:0045976 GO:0045976
## GO:0061047 GO:0061047
## GO:0072053 GO:0072053
## GO:0072054 GO:0072054
## GO:2000017 GO:2000017
##                                                                                                  Description
## GO:0003340 negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis
## GO:0045976                                              negative regulation of mitotic cell cycle, embryonic
## GO:0061047                                   positive regulation of branching involved in lung morphogenesis
## GO:0072053                                                                   renal inner medulla development
## GO:0072054                                                                   renal outer medulla development
## GO:2000017                                           positive regulation of determination of dorsal identity
##            GeneRatio BgRatio       pvalue    p.adjust qvalue geneID Count
## GO:0003340       1/1 2/18888 0.0001058873 0.003925395     NA CTNNB1     1
## GO:0045976       1/1 2/18888 0.0001058873 0.003925395     NA CTNNB1     1
## GO:0061047       1/1 2/18888 0.0001058873 0.003925395     NA CTNNB1     1
## GO:0072053       1/1 2/18888 0.0001058873 0.003925395     NA CTNNB1     1
## GO:0072054       1/1 2/18888 0.0001058873 0.003925395     NA CTNNB1     1
## GO:2000017       1/1 2/18888 0.0001058873 0.003925395     NA CTNNB1     1
##                    ID                    Description GeneRatio BgRatio
## GO:0034750 GO:0034750 Scrib-APC-beta-catenin complex       1/1 2/19894
## GO:1990711 GO:1990711      beta-catenin-ICAT complex       1/1 2/19894
## GO:0070369 GO:0070369    beta-catenin-TCF7L2 complex       1/1 3/19894
## GO:0071664 GO:0071664         catenin-TCF7L2 complex       1/1 4/19894
## GO:0005916 GO:0005916                fascia adherens       1/1 9/19894
## GO:0016600 GO:0016600              flotillin complex       1/1 9/19894
##                  pvalue    p.adjust qvalue geneID Count
## GO:0034750 0.0001005328 0.003166784     NA CTNNB1     1
## GO:1990711 0.0001005328 0.003166784     NA CTNNB1     1
## GO:0070369 0.0001507992 0.003166784     NA CTNNB1     1
## GO:0071664 0.0002010656 0.003166784     NA CTNNB1     1
## GO:0005916 0.0004523977 0.004318342     NA CTNNB1     1
## GO:0016600 0.0004523977 0.004318342     NA CTNNB1     1
##                    ID
## GO:0003810 GO:0003810
## GO:0016811 GO:0016811
## GO:0016410 GO:0016410
## GO:0016810 GO:0016810
## GO:0140993 GO:0140993
## GO:0016747 GO:0016747
##                                                                                        Description
## GO:0003810                                    protein-glutamine gamma-glutamyltransferase activity
## GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
## GO:0016410                                                              N-acyltransferase activity
## GO:0016810                   hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
## GO:0140993                                                              histone modifying activity
## GO:0016747              acyltransferase activity, transferring groups other than amino-acyl groups
##            GeneRatio   BgRatio       pvalue    p.adjust qvalue geneID Count
## GO:0003810       1/1   9/18522 0.0004859086 0.004859086     NA   TGM2     1
## GO:0016811       1/1  72/18522 0.0038872692 0.017096786     NA   TGM2     1
## GO:0016410       1/1  95/18522 0.0051290357 0.017096786     NA   TGM2     1
## GO:0016810       1/1 134/18522 0.0072346399 0.018086600     NA   TGM2     1
## GO:0140993       1/1 207/18522 0.0111758989 0.020336177     NA   TGM2     1
## GO:0016747       1/1 226/18522 0.0122017061 0.020336177     NA   TGM2     1
##                    ID
## GO:0018277 GO:0018277
## GO:0060605 GO:0060605
## GO:0060662 GO:0060662
## GO:0032471 GO:0032471
## GO:0071314 GO:0071314
## GO:2000425 GO:2000425
##                                                                       Description
## GO:0018277                                                    protein deamination
## GO:0060605                                                  tube lumen cavitation
## GO:0060662                                              salivary gland cavitation
## GO:0032471 negative regulation of endoplasmic reticulum calcium ion concentration
## GO:0071314                                           cellular response to cocaine
## GO:2000425                                 regulation of apoptotic cell clearance
##            GeneRatio  BgRatio       pvalue    p.adjust qvalue geneID Count
## GO:0018277       1/1  2/18888 0.0001058873 0.004575846     NA   TGM2     1
## GO:0060605       1/1  5/18888 0.0002647183 0.004575846     NA   TGM2     1
## GO:0060662       1/1  5/18888 0.0002647183 0.004575846     NA   TGM2     1
## GO:0032471       1/1  8/18888 0.0004235493 0.004575846     NA   TGM2     1
## GO:0071314       1/1 10/18888 0.0005294367 0.004575846     NA   TGM2     1
## GO:2000425       1/1 10/18888 0.0005294367 0.004575846     NA   TGM2     1
##                    ID                              Description GeneRatio
## GO:0000786 GO:0000786                               nucleosome       1/1
## GO:0005925 GO:0005925                           focal adhesion       1/1
## GO:0062023 GO:0062023 collagen-containing extracellular matrix       1/1
## GO:0030055 GO:0030055                  cell-substrate junction       1/1
##              BgRatio      pvalue   p.adjust qvalue geneID Count
## GO:0000786 135/19894 0.006785966 0.02166482     NA   TGM2     1
## GO:0005925 421/19894 0.021162159 0.02166482     NA   TGM2     1
## GO:0062023 428/19894 0.021514024 0.02166482     NA   TGM2     1
## GO:0030055 431/19894 0.021664824 0.02166482     NA   TGM2     1
barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, bicluster 1")

barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, bicluster 2")

barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, bicluster 3")

barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, bicluster 4")

barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, bicluster 5")

barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, bicluster 8")

barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, bicluster 10")

barplot(ego_MF[[8]], title = "enrichGO, Molecular Function, bicluster 12")

barplot(ego_MF[[9]], title = "enrichGO, Molecular Function, bicluster 16")

barplot(ego_MF[[10]], title = "enrichGO, Molecular Function, bicluster 18")

barplot(ego_MF[[11]], title = "enrichGO, Molecular Function, bicluster 22")

barplot(ego_MF[[12]], title = "enrichGO, Molecular Function, bicluster 26")

barplot(ego_MF[[13]], title = "enrichGO, Molecular Function, bicluster 28")

barplot(ego_BP[[1]], title = "enrichGO, Biological Process, bicluster 1")

barplot(ego_BP[[2]], title = "enrichGO, Biological Process, bicluster 2")

barplot(ego_BP[[3]], title = "enrichGO, Biological Process, bicluster 3")

barplot(ego_BP[[4]], title = "enrichGO, Biological Process, bicluster 4")

barplot(ego_BP[[5]], title = "enrichGO, Biological Process, bicluster 5")

barplot(ego_BP[[6]], title = "enrichGO, Biological Process, bicluster 8")

barplot(ego_BP[[7]], title = "enrichGO, Biological Process, bicluster 10")

barplot(ego_BP[[8]], title = "enrichGO, Biological Process, bicluster 12")

barplot(ego_BP[[9]], title = "enrichGO, Biological Process, bicluster 16")

barplot(ego_BP[[10]], title = "enrichGO, Biological Process, bicluster 18")

barplot(ego_BP[[11]], title = "enrichGO, Biological Process, bicluster 22")

barplot(ego_BP[[12]], title = "enrichGO, Biological Process, bicluster 26")

barplot(ego_BP[[13]], title = "enrichGO, Biological Process, bicluster 28")

barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, bicluster 1")

barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, bicluster 2")

barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, bicluster 3")

barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, bicluster 4")

barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, bicluster 5")

barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, bicluster 8")

barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, bicluster 10")

barplot(ego_CC[[8]], title = "enrichGO, Cellular Component, bicluster 12")

barplot(ego_CC[[9]], title = "enrichGO, Cellular Component, bicluster 16")

barplot(ego_CC[[10]], title = "enrichGO, Cellular Component, bicluster 18")

barplot(ego_CC[[11]], title = "enrichGO, Cellular Component, bicluster 22")

barplot(ego_CC[[12]], title = "enrichGO, Cellular Component, bicluster 26")

barplot(ego_CC[[13]], title = "enrichGO, Cellular Component, bicluster 28")

DAG plots for ego

goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, bicluster 1")

goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, bicluster 2")

goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, bicluster 3")

goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, bicluster 4")

goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, bicluster 5")

goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, bicluster 8")

goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, bicluster 10")

goplot(ego_MF[[8]]) + labs(title = "enrichGO, Molecular Function, bicluster 12")

goplot(ego_MF[[9]]) + labs(title = "enrichGO, Molecular Function, bicluster 16")

goplot(ego_MF[[10]]) + labs(title = "enrichGO, Molecular Function, bicluster 18")

goplot(ego_MF[[11]]) + labs(title = "enrichGO, Molecular Function, bicluster 22")

goplot(ego_MF[[12]]) + labs(title = "enrichGO, Molecular Function, bicluster 26")

goplot(ego_MF[[13]]) + labs(title = "enrichGO, Molecular Function, bicluster 28")

goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, bicluster 1")
## Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, bicluster 2")

goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, bicluster 3")
## Warning: ggrepel: 15 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, bicluster 4")

goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, bicluster 5")

goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, bicluster 8")
## Warning: ggrepel: 15 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, bicluster 10")
## Warning: ggrepel: 15 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[8]]) + labs(title = "enrichGO, Biological Process, bicluster 12")
## Warning: ggrepel: 15 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[9]]) + labs(title = "enrichGO, Biological Process, bicluster 16")

goplot(ego_BP[[10]]) + labs(title = "enrichGO, Biological Process, bicluster 18")
## Warning: ggrepel: 65 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[11]]) + labs(title = "enrichGO, Biological Process, bicluster 22")
## Warning: ggrepel: 71 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[12]]) + labs(title = "enrichGO, Biological Process, bicluster 26")
## Warning: ggrepel: 78 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[13]]) + labs(title = "enrichGO, Biological Process, bicluster 28")
## Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, bicluster 1")

goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, bicluster 2")

goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, bicluster 3")

goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, bicluster 4")

goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, bicluster 5")

goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, bicluster 8")

goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, bicluster 10")

goplot(ego_CC[[8]]) + labs(title = "enrichGO, Cellular Component, bicluster 12")

goplot(ego_CC[[9]]) + labs(title = "enrichGO, Cellular Component, bicluster 16")

goplot(ego_CC[[10]]) + labs(title = "enrichGO, Cellular Component, bicluster 18")

goplot(ego_CC[[11]]) + labs(title = "enrichGO, Cellular Component, bicluster 22")

goplot(ego_CC[[12]]) + labs(title = "enrichGO, Cellular Component, bicluster 26")

goplot(ego_CC[[13]]) + labs(title = "enrichGO, Cellular Component, bicluster 28")

3. Export Pathway Analysis result to data

pathway = list("ggo_MF" = ggo_MF,
               "ggo_BP" = ggo_BP,
               "ggo_CC" = ggo_CC,
               "ego_MF" = ego_MF,
               "ego_BP" = ego_BP,
               "ego_CC" = ego_CC)

saveRDS(pathway, file = "data/out_pathway/pathways_superbiclust.fabia.rds")